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- PDB-9jfi: Structure of wild type catalytic domains of threonine deaminase i... -

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Basic information

Entry
Database: PDB / ID: 9jfi
TitleStructure of wild type catalytic domains of threonine deaminase in complex with PLP
ComponentsL-threonine dehydratase biosynthetic IlvA
KeywordsSTRUCTURAL PROTEIN / Threonine Deaminase / PLP
Function / homology
Function and homology information


threonine ammonia-lyase / threonine deaminase activity / threonine metabolic process / branched-chain amino acid biosynthetic process / isoleucine biosynthetic process / amino acid binding / pyridoxal phosphate binding
Similarity search - Function
Threonine dehydratase, biosynthetic / Threonine dehydratase, ACT-like domain / Threonine dehydratase, ACT-like domain superfamily / C-terminal regulatory domain of Threonine dehydratase / ACT-like domain profile. / : / Serine/threonine dehydratase, pyridoxal-phosphate-binding site / Serine/threonine dehydratases pyridoxal-phosphate attachment site. / ACT-like domain / Pyridoxal-phosphate dependent enzyme ...Threonine dehydratase, biosynthetic / Threonine dehydratase, ACT-like domain / Threonine dehydratase, ACT-like domain superfamily / C-terminal regulatory domain of Threonine dehydratase / ACT-like domain profile. / : / Serine/threonine dehydratase, pyridoxal-phosphate-binding site / Serine/threonine dehydratases pyridoxal-phosphate attachment site. / ACT-like domain / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme
Similarity search - Domain/homology
L-threonine dehydratase biosynthetic IlvA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKhodi, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Dimer-Tetramer Transition Modulates the allosteric regulation of Threonine Deaminase
Authors: Khodi, S. / Yekeen, H. / Liu, H. / Chen, Q.
History
DepositionSep 4, 2024Deposition site: PDBJ / Processing site: PDBC
SupersessionMay 14, 2025ID: 8ZLV
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-threonine dehydratase biosynthetic IlvA
B: L-threonine dehydratase biosynthetic IlvA


Theoretical massNumber of molelcules
Total (without water)70,3952
Polymers70,3952
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-12 kcal/mol
Surface area24580 Å2
MethodPISA
2
A: L-threonine dehydratase biosynthetic IlvA
B: L-threonine dehydratase biosynthetic IlvA

A: L-threonine dehydratase biosynthetic IlvA
B: L-threonine dehydratase biosynthetic IlvA


Theoretical massNumber of molelcules
Total (without water)140,7894
Polymers140,7894
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7350 Å2
ΔGint-46 kcal/mol
Surface area46240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.159, 102.159, 116.473
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein L-threonine dehydratase biosynthetic IlvA / Threonine deaminase


Mass: 35197.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: ilvA, b3772, JW3745 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04968, threonine ammonia-lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43.96 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M CaCl2H4O2, 0.1 M HEPES sodium pH 7.5 and 28% v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.9→45.69 Å / Num. obs: 14225 / % possible obs: 99.76 % / Redundancy: 20.3 % / Biso Wilson estimate: 72.07 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.23 / Rpim(I) all: 0.04859 / Rrim(I) all: 0.2428 / Net I/σ(I): 15.1
Reflection shellResolution: 2.9→3.004 Å / Mean I/σ(I) obs: 1.71 / Num. unique obs: 1409 / CC1/2: 0.643 / CC star: 0.885 / Rpim(I) all: 0.4421 / Rrim(I) all: 0.232 / Χ2: 0.885 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→45.69 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2723 740 5.21 %0.2614
Rwork0.2237 ---
obs-14200 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→45.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4835 0 0 7 4842
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044920
X-RAY DIFFRACTIONf_angle_d0.6686663
X-RAY DIFFRACTIONf_dihedral_angle_d7.032703
X-RAY DIFFRACTIONf_chiral_restr0.045763
X-RAY DIFFRACTIONf_plane_restr0.005871
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.120.35061390.28342638X-RAY DIFFRACTION100
3.12-3.440.31651450.25822658X-RAY DIFFRACTION100
3.44-3.940.29921640.24632624X-RAY DIFFRACTION99
3.94-4.960.2551430.18852686X-RAY DIFFRACTION100
4.96-45.690.24141490.2032854X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0768-1.68180.5073.4106-1.11723.23430.1744-0.2499-0.2395-0.1926-0.05440.1822-0.0411-0.2275-0.16580.31320.0080.04490.3957-0.02410.297820.845.9290.985
24.57081.2313-2.38022.36080.0275.6968-0.39270.7929-0.0032-0.58280.23540.2216-0.1789-0.52470.19050.4505-0.0584-0.09210.4319-0.02510.282121.3333.834-19.32
32.93450.3354-0.56141.94160.28744.5166-0.21630.2992-0.4683-0.2932-0.0893-0.05710.0999-0.08540.14210.2503-0.00870.05110.2371-0.00270.415128.4694.949-10.176
41.8161-0.1918-0.7868.06141.77930.50990.0040.31240.0858-0.65950.4254-0.6315-0.37920.0265-0.49640.51120.05830.1140.78920.16290.609945.4241.272-10.237
54.53251.8756-0.70071.95590.70712.25750.0062-0.4617-0.9877-0.59560.1527-0.7269-0.4559-0.12140.0730.3868-0.024-0.00180.45260.13510.452338.5644.47-6.543
61.5883-0.98510.69123.7262-1.35832.72940.12590.1634-0.3204-0.1252-0.1396-0.11430.33940.2370.00120.38830.00860.07910.45890.02870.539228.436-9.4973.928
73.3877-1.9744-0.26432.8633-0.17464.79530.0349-0.1717-0.439-0.34680.01890.23060.23360.1814-0.20870.4442-0.0099-0.0740.3269-0.03830.4672-1.448-17.5950.303
81.2021-0.08111.90246.1015-0.26926.6948-0.3134-0.4866-0.31980.5550.91690.32580.2860.579-0.41290.57060.19360.08390.7793-0.05050.61583.968-26.45519.656
93.5765-1.3002-2.14483.0650.16472.447-0.06280.1597-0.6415-0.2061-0.05710.5350.2397-0.01330.12250.5931-0.0237-0.2060.4557-0.11910.7807-4.204-30.729-2.354
103.10151.68030.23354.40550.77423.44270.40.2822-0.4338-0.4011-0.2449-0.03230.25360.3127-0.10140.63980.1367-0.03930.4165-0.05730.386912.134-24.421-8.113
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 10:55 )A10 - 55
2X-RAY DIFFRACTION2( CHAIN A AND RESID 56:114 )A56 - 114
3X-RAY DIFFRACTION3( CHAIN A AND RESID 115:217 )A115 - 217
4X-RAY DIFFRACTION4( CHAIN A AND RESID 218:237 )A218 - 237
5X-RAY DIFFRACTION5( CHAIN A AND RESID 238:266 )A238 - 266
6X-RAY DIFFRACTION6( CHAIN A AND RESID 267:335 )A267 - 335
7X-RAY DIFFRACTION7( CHAIN B AND RESID 12:72 )B12 - 72
8X-RAY DIFFRACTION8( CHAIN B AND RESID 73:159 )B73 - 159
9X-RAY DIFFRACTION9( CHAIN B AND RESID 160:266 )B160 - 266
10X-RAY DIFFRACTION10( CHAIN B AND RESID 267:334 )B267 - 334

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